2016-06-27 13:37 GMT-06:00 Chang Woon Jang <[email protected]>: > Dear Christoph, > > > I tested the following command. > > csg_dump --top topol.tpr --excl > exclusion_list > > In the exclusion_list file, the number are listed like > > I have 15000 beads in 300 molecules > > List of exclusions: > 1 2 3 4 5 6 7 8 9 10 11 12 > 2 3 4 5 6 7 9 > 3 4 5 6 7 9 > 4 5 6 7 9 > 5 6 7 8 9 10 11 12 13 > 6 7 8 9 10 11 12 > 7 8 9 10 11 12 > 8 9 > 9 10 11 12 13 14 21 > 10 11 12 13 > 11 12 13 > 12 13 14 15 16 19 21 22 > 13 14 15 16 17 19 20 21 22 > 18 13 14 15 16 17 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 40 > ... > > > What do these numbers mean? The first line has 1 2 3 4 5 6 7 8 9 10 11 12. I > do not know what this series of numbers. It means, atom #1 is exclude with 2, 3, 4, ...
> > However, it seems that csg_stat excluded the pairs of beads directly bonded. > Therefore, I do not need consider the 1-3 interactions in CG system in > lammps. > > > I am not sure why the density is higher than atomistic reference density > when I do not apply 1-3 interactions. I have driven tabulated potential > using ibi pressure correction method. Are there any suggestions for better > CG simulation to fix the density? > > Thank you. > > Best regards, > Changwoon Jang > > > > On Mon, Jun 27, 2016 at 3:15 PM, Christoph Junghans <[email protected]> > wrote: >> >> 2016-06-27 12:58 GMT-06:00 Chang Woon Jang <[email protected]>: >> > Dear VOTCA users, >> > >> > I have a question about radial distribution functions from csg_stat. >> > >> > I have obtained radial distribution functions and used them for >> > iterative >> > boltzmann inversion to derive non-bonded tabulated potentials. After >> > some >> > iterations, the calculated radial distribution functions were well >> > matched >> > with reference RDF from csg_stat. Then, I used the obtained tabulated >> > potentials for lammps simulations. >> > >> > From the lammps simulation with tabulated potentials, the liquid >> > polymer >> > system has higher density (1.3 g/cc) than the experimental density (1.07 >> > g/cc) when I do not consider 1-3 bead pairs which are those separated by >> > 3 >> > bonds. However, when I applied 1-3 interactions, the simulational >> > density is >> > in good agreement with experimental density. >> > >> > I think that the reference radial distribution functions from >> > csg_stat >> > are calculated with pairs of beads directly bonded to each other as well >> > as >> > non-bonded pairs. >> > >> > Is this correct? >> This depends on your topology file. csg_stat excludes bonds and angles >> automatically. >> However, if you have a topology file without bonds and angles, they >> wont' be excluded. >> To check use: >> $ csg_dump --top topol.xml --excl >> >> Christoph >> > >> > Thank you. >> > >> > Best regards, >> > Changwoon Jang >> > >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To post to this group, send email to [email protected]. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
